TBLASTN 2.2.17 [Aug-26-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|212646307|ref|NP_001129887.1| SEC(selenocysteine)-tRNA
Synthase family member (secs-1) [Caenorhabditis elegans]
         (523 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_12                                                           159   6e-39

>scaffold_12
          Length = 1412611

 Score =  159 bits (403), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 95/271 (35%), Positives = 138/271 (50%), Gaps = 35/271 (12%)
 Frame = +1

Query: 74     QIPEEGWSEHTLDLFLSWLSSHDTNNRVDMIPVGAGEREGRVLTPLVQRLHSNLTHGIGR 133
              ++PE GW E  ++  L   ++ D+NN  +   VG GERE RV++PLV+R H  L HG+GR
Sbjct: 891142 KLPEAGWREEDIEALLRNCAAMDSNNFGN--NVGVGEREARVISPLVRRRHFGLAHGVGR 891315

Query: 134    SGNLLEIQPKALGSSMLACLSNEFXXXXXXXXXXXXVKSCIVVPLCTGMSLSLCMTSWRR 193
              SG++  +QPKA GSS+LA LSN                + +V+P  TG+SL+LC+ S R 
Sbjct: 891316 SGDIAAVQPKAAGSSLLAKLSNHLALDALREAGNTEFTAALVLPCATGLSLALCLLSVRN 891495

Query: 194    RRPKA--KYVVWLRIDQKSSLKSIYHAGFEPIIVEPIRDR-------------------- 231
              R   A  K V+W RIDQKS  K I  AG EP++V P RDR                    
Sbjct: 891496 RPGNASKKKVLWCRIDQKSCFKGILLAGLEPVVVSPTRDRGVGSPPDHARLLKKKKAKGA 891675

Query: 232    -------------DSLITDVETVNRIIEQRGEEILCVMTTTSCFAPRSPDNVEAISAICA 278
                           D L+TD+  +   ++  G+++L V+TTTSCFAPR+P   E   +   
Sbjct: 891676 DAPPPPPPPSGLGDELLTDLPALEARLDALGDDVLAVVTTTSCFAPRAPGQ-ETSDSSSL 891852

Query: 279    AHDVPHLVNNAYGLQSEETIRKIAAAHECGR 309
               H+      +   + +   +R++ A     R
Sbjct: 891853 QHECSARARSGKSIHASRALREMIARPRISR 891945



 Score =  155 bits (391), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 93/265 (35%), Positives = 142/265 (53%), Gaps = 24/265 (9%)
 Frame = +3

Query: 260    SCFAPR-SPDNVEAISAICAAHDVPHLVNNAYGLQSEETIRKIAAAHECGRVDAVVQSLD 318
              + F PR +PD+V A++ +CAA +V H+VNNAYG+Q   +   ++ A   GRVD VVQS D
Sbjct: 891996 TLFLPRRAPDDVAAVARLCAAREVAHVVNNAYGVQCARSSATLSRACRVGRVDLVVQSTD 892175

Query: 319    KNFQVPVGGAVIAAFKQNHIQSIAQSYPGRASSVPSRDLVLTLLYQGQSAFLEPFGKQKQ 378
              KNF VPVGGAV+A+     +  + + YPGRAS+ PS+DL++TLL  G+  + +    ++ 
Sbjct: 892176 KNFLVPVGGAVVASPDAALVAEVGRGYPGRASATPSQDLLVTLLGLGRRGWRDLLDGREA 892355

Query: 379    MFLKMRRKLISFAENIGECVYEVPENEISSAMT----------------------LSTIP 416
              +      KL + A   GE V E P N IS  +T                         + 
Sbjct: 892356 LLDAFGAKLRALAAKHGERVLETPHNRISFGVTLERLAAAAAELQRAEGADDAAAARRLA 892535

Query: 417    PAKQTLFGSILFAKGITGARVVTSSQSKTTIEGCE-FINFGSHTTEQHGGYLNIACSVGM 475
                K T FGS+LF + ++G RVV  +  KT + G E F  FG+   +    Y  +A ++G+
Sbjct: 892536 NDKVTKFGSMLFTRCVSGTRVV--APGKTQVIGPETFRGFGASADDYPVPYFTVAVALGV 892709

Query: 476    TDHELEELFTRLTSSYAKFVRELAK 500
                 EL++   RL  ++  F +++ K
Sbjct: 892710 APEELDDFLGRLDKTFLHFHKQIGK 892784


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
   0.319    0.133    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1185
Number of Hits to DB: 38,631,024
Number of extensions: 595677
Number of successful extensions: 3795
Number of sequences better than 10.0: 3
Number of HSP's gapped: 3792
Number of HSP's successfully gapped: 5
Length of query: 523
Length of database: 18,886,859
Length adjustment: 109
Effective length of query: 414
Effective length of database: 18,757,694
Effective search space: 7765685316
Effective search space used: 7765685316
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)TBLASTN 2.2.17 [Aug-26-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= gi|194209254|ref|XP_001497613.2| PREDICTED: similar to
O-phosphoseryl-tRNA(Sec) selenium transferase (Selenocysteine
synthase) (Sec synthase) (Selenocysteinyl-tRNA(Sec) synthase)
(Sep-tRNA:Sec-tRNA synthase) (SepSecS) (UGA suppressor tRNA-associated
protein) (tRNA(Ser/Sec)-associated antigen [Equus caballus]
         (505 letters)

Database: genome.fa 
           1185 sequences; 56,660,578 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

scaffold_12                                                           215   1e-55
scaffold_7                                                             32   1.5  
scaffold_35                                                            32   1.8  

>scaffold_12
          Length = 1412611

 Score =  215 bits (547), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 123/267 (46%), Positives = 154/267 (57%), Gaps = 35/267 (13%)
 Frame = +1

Query: 1      MNRESFAAGERLVSPAYVRQGHEARRSHEHLIRLLLEKGKCPEDGWDESTLELFLHELAI 60
              M +E +AA  +LV    V Q  +   S+    R L+E  K PE GW E  +E  L   A 
Sbjct: 891025 MEKEFYAAAAQLVDAHIVAQAQQVASSNAAPARRLVESKKLPEAGWREEDIEALLRNCAA 891204

Query: 61     MDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNS 120
              MDSNNF  N GVGERE RV S LV RRH+   HG+GRSGDI+AVQPKAAGSSLL K++N 
Sbjct: 891205 MDSNNFGNNVGVGEREARVISPLVRRRHFGLAHGVGRSGDIAAVQPKAAGSSLLAKLSNH 891384

Query: 121    LVLDIIKLAGVHTVSNCFVVPMATGMSLTLCFLTLRHKRPKA--KYIIWPRIDQKSCFKS 178
              L LD ++ AG    +   V+P ATG+SL LC L++R++   A  K ++W RIDQKSCFK 
Sbjct: 891385 LALDALREAGNTEFTAALVLPCATGLSLALCLLSVRNRPGNASKKKVLWCRIDQKSCFKG 891564

Query: 179    MITAGFEPVVIENVLE---------------------------------GDELRTDLKAV 205
              ++ AG EPVV+    +                                 GDEL TDL A+
Sbjct: 891565 ILLAGLEPVVVSPTRDRGVGSPPDHARLLKKKKAKGADAPPPPPPPSGLGDELLTDLPAL 891744

Query: 206    EAKVQELGPDYVLCVHSTTSCFAPRVP 232
              EA++  LG D VL V +TTSCFAPR P
Sbjct: 891745 EARLDALGDD-VLAVVTTTSCFAPRAP 891822



 Score =  205 bits (522), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 108/260 (41%), Positives = 152/260 (58%), Gaps = 20/260 (7%)
 Frame = +3

Query: 225    SCFAPR-VPDRVEQLAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLD 283
              + F PR  PD V  +A +CA  ++ H+VNNAYGVQ ++    + +  RVGR+D  VQS D
Sbjct: 891996 TLFLPRRAPDDVAAVARLCAAREVAHVVNNAYGVQCARSSATLSRACRVGRVDLVVQSTD 892175

Query: 284    KNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGYKKLLKERKE 343
              KNF+VPVGGA++A  + + + E+ + YPGRASA+PS D+L+TLL LG  G++ LL  R+ 
Sbjct: 892176 KNFLVPVGGAVVASPDAALVAEVGRGYPGRASATPSQDLLVTLLGLGRRGWRDLLDGREA 892355

Query: 344    MFSYLSNQLKKLSEAYNERLLHTPHNPISLAVTLKTLDEHREKA---------------- 387
              +      +L+ L+  + ER+L TPHN IS  VTL+ L     +                 
Sbjct: 892356 LLDAFGAKLRALAAKHGERVLETPHNRISFGVTLERLAAAAAELQRAEGADDAAAARRLA 892535

Query: 388    ---VTQLGSMLFTRQVSGARVVPLGSVQTVSGYAFRGFMSHTDNYPCAYLNAASAIGMKT 444
                 VT+ GSMLFTR VSG RVV  G  Q +    FRGF +  D+YP  Y   A A+G+  
Sbjct: 892536 NDKVTKFGSMLFTRCVSGTRVVAPGKTQVIGPETFRGFGASADDYPVPYFTVAVALGVAP 892715

Query: 445    QDVDLFIKRLDKCLKTIRKE 464
              +++D F+ RLDK      K+
Sbjct: 892716 EELDDFLGRLDKTFLHFHKQ 892775


>scaffold_7
          Length = 2177197

 Score = 32.3 bits (72), Expect = 1.5,   Method: Composition-based stats.
 Identities = 49/190 (25%), Positives = 79/190 (41%), Gaps = 13/190 (6%)
 Frame = -1

Query: 254    AYGVQSSKCMHLIQQGAR----VGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKM 309
              ++ VQ+   M++  Q A     +GRI     +LD++F         A +  S   E  K+
Sbjct: 926989 SHNVQTVCAMNVHAQDANADGVLGRIG---DALDESF---------AAY--SIFGEEPKV 926852

Query: 310    YPGRASASPSLDVLITLLSLGSNGYKKLLKERKEMFSYLSNQLKK--LSEAYNERLLHTP 367
                G A   P  D+L    S G  G   + +  +     L++++     SE Y ER +   
Sbjct: 926851 LEGAAGLRPVADILA---SFGVAGLADVARTLESSIRALTSKVSTSIFSETYAERTISAI 926681

Query: 368    HNPISLAVTLKT--LDEHREKAVTQLGSML-----FTRQVSGARVVPLGSVQTVSGYAFR 420
                  +L  TLK   L   R +A++Q   ++       R + G     LGS + V      
Sbjct: 926680 DRSYALDATLKAHELVNGRCEALSQNRDLMDQFEQVDRLIRGKD--QLGSSRAVFHVQLD 926507

Query: 421    GFMSHTDNYP 430
              GF +H+DN P
Sbjct: 926506 GFDTHSDNGP 926477


>scaffold_35
          Length = 443549

 Score = 32.0 bits (71), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/40 (40%), Positives = 21/40 (52%)
 Frame = -1

Query: 71     GVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAG 110
              GVG R  R A+  +  R    + G  R GD+ AV+P A G
Sbjct: 366683 GVGHRAAREAAVALEERVALEVDGFERRGDLRAVEPAARG 366564


  Database: genome.fa
    Posted date:  Feb 16, 2009  1:41 PM
  Number of letters in database: 56,660,578
  Number of sequences in database:  1185
  
Lambda     K      H
   0.320    0.135    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1185
Number of Hits to DB: 31,861,836
Number of extensions: 455888
Number of successful extensions: 3212
Number of sequences better than 10.0: 10
Number of HSP's gapped: 3208
Number of HSP's successfully gapped: 12
Length of query: 505
Length of database: 18,886,859
Length adjustment: 109
Effective length of query: 396
Effective length of database: 18,757,694
Effective search space: 7428046824
Effective search space used: 7428046824
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)
